Mitochondrial genomes revisited: why do different lineages retain different genes?

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: Jan. 25, 2024

Abstract The mitochondria contain their own genome derived from an alphaproteobacterial endosymbiont. From thousands of protein-coding genes originally encoded by ancestor, only between 1 and about 70 are on extant mitochondrial genomes (mitogenomes). Thanks to a dramatically increasing number sequenced annotated mitogenomes coherent picture why some were lost, or relocated the nucleus, is emerging. In this review, we describe characteristics mitochondria-to-nucleus gene transfer resulting varied content across eukaryotes. We introduce ‘burst-upon-drift’ model best explain nuclear-mitochondrial population genetics with flares due genetic drift.

Language: Английский

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Is the Mutation Rate Lower in Genomic Regions of Stronger Selective Constraints?

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(8)

Published: July 30, 2022

Abstract A study of the plant Arabidopsis thaliana detected lower mutation rates in genomic regions where mutations are more likely to be deleterious, challenging principle that mutagenesis is blind its consequence. To examine generality this finding, we analyze large mutational data from baker's yeast and humans. The do not exhibit trend, whereas human show an opposite trend disappears upon control potential confounders. We find identified substantially than reported original data-generating studies expected Arabidopsis' rate. These extra enriched polynucleotide tracts have relatively low sequencing qualities so errors. Furthermore, “mutations” can produce purported Arabidopsis. Together, our results support stronger selective constraints plant, fungal, animal models examined.

Language: Английский

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DNA fun facts: Hypermutable DNA, mutagenic DNA break repair, and transcription-associated mutagenesis

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 31 - 78

Published: Jan. 1, 2025

Language: Английский

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Spontaneous and environment induced genomic alterations in yeast model

Cell Insight, Journal Year: 2024, Volume and Issue: 4(1), P. 100209 - 100209

Published: Sept. 26, 2024

Language: Английский

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Mutations in yeast are deleterious on average regardless of the degree of adaptation to the testing environment

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 11, 2024

Abstract The role of spontaneous mutations in evolution depends on the distribution their effects fitness. Despite a general consensus that new are deleterious average, handful mutation accumulation experiments diverse organisms instead suggest beneficial and can have comparable fitness impacts, i.e., product respective rates be roughly equal. We currently lack framework for predicting when such pattern will occur. One idea is more evident genotypes not well adapted to testing environment. tested this prediction experimentally laboratory yeast Saccharomyces cerevisiae by allowing nine replicate populations adapt novel environments with complex sets stressors. After >1000 asexual generations interspersed 41 rounds sexual reproduction, we assessed mean effect induced growth both environment which they had been adapting alternative were severity depending However, find no evidence adaptive match between genotype predictive mutational effects.

Language: Английский

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Spontaneous single-nucleotide substitutions and microsatellite mutations have distinct distributions of fitness effects

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(7), P. e3002698 - e3002698

Published: July 1, 2024

The fitness effects of new mutations determine key properties evolutionary processes. Beneficial drive evolution, yet selection is also shaped by the frequency small-effect deleterious mutations, whose combined effect can burden otherwise adaptive lineages and alter trajectories outcomes in clonally evolving organisms such as viruses, microbes, tumors. small sizes these important have made accurate measurements their rates difficult. In assessing on growth be especially instructive, this complex phenotype closely linked to organisms. Here, we perform high-throughput time-lapse microscopy cells from mutation-accumulation strains precisely infer distribution mutational rate budding yeast, Saccharomyces cerevisiae . We show that are overwhelmingly negative, highly skewed towards very sizes, frequent enough suggest hitchhikers may impose a significant lineages. By using lines accumulated either wild-type or slippage repair-defective backgrounds, further disentangle 2 common types single-nucleotide substitutions simple sequence repeat indels, they distinct yeast rate. Although average mutation (approximately 0.3%), many do rate, implying class has an impact.

Language: Английский

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Two independent DNA repair pathways cause mutagenesis in template switching deficientSaccharomyces cerevisiae

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: June 26, 2023

Abstract Upon DNA replication stress, cells utilize the post-replication repair pathway to single-stranded and maintain genome integrity. Post-replication is divided into two branches: error-prone translesion synthesis, signaled by PCNA mono-ubiquitination, error-free template switching, poly-ubiquitination. In Saccharomyces cerevisiae , Rad5 involved in both branches of during stress. When poly-ubiquitination function disrupted, recruits synthesis polymerases stalled forks, resulting mutagenic repair. Details how carried out, as well relationship between Rad5-mediated canonical PCNA-mediated repair, remain be understood. We find that requires polymerase ζ but does not require other yeast activities. Furthermore, we show independent binding Rev1 so separable from absence modes contribute additively stress response a timing-independent manner. Cellular contexts where switching compromised are simply laboratory phenomena, natural variant RAD5 defective therefore Rad5- Our results highlight importance regulating spontaneous mutagenesis genetic diversity S. through different

Language: Английский

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Spontaneous single-nucleotide substitutions and microsatellite mutations have distinct distributions of fitness effects

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 4, 2023

Abstract The fitness effects of new mutations determine key properties evolutionary processes. Beneficial drive evolution, yet selection is also shaped by the frequency small-effect deleterious mutations, whose combined effect can burden otherwise adaptive lineages and alter trajectories outcomes in clonally evolving organisms such as viruses, microbes, tumors. small sizes these important have made accurate measurements their rates difficult. In assessing on growth be especially instructive, this complex phenotype closely linked to organisms. Here, we perform high-throughput time-lapse microscopy cells from mutation-accumulation strains precisely infer distribution mutational rate budding yeast, Saccharomyces cerevisiae . We show that are overwhelmingly negative, highly skewed towards very sizes, frequent enough suggest hitchhikers may impose a significant lineages. By using lines accumulated either wild-type or slippage repair-defective backgrounds, further disentangle two common types single-nucleotide substitutions simple sequence repeat indels, they distinct yeast rate. Although average mutation (∼0.3%), many do rate, implying class has an impact.

Language: Английский

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Two independent DNA repair pathways cause mutagenesis in template switching deficient Saccharomyces cerevisiae

Genetics, Journal Year: 2023, Volume and Issue: 225(3)

Published: Aug. 18, 2023

Abstract Upon DNA replication stress, cells utilize the postreplication repair pathway to single-stranded and maintain genome integrity. Postreplication is divided into 2 branches: error-prone translesion synthesis, signaled by proliferating cell nuclear antigen (PCNA) monoubiquitination, error-free template switching, PCNA polyubiquitination. In Saccharomyces cerevisiae, Rad5 involved in both branches of during stress. When polyubiquitination function s disrupted, recruits synthesis polymerases stalled forks, resulting mutagenic repair. Details how carried out, as well relationship between Rad5-mediated canonical PCNA-mediated repair, remain be understood. We find that requires polymerase ζ but does not require other yeast activities. Furthermore, we show independent binding Rev1 so separable from absence modes contribute additively stress response a timing-independent manner. Cellular contexts where switching compromised are simply laboratory phenomena, natural variant RAD5 defective therefore Rad5- Our results highlight importance regulating spontaneous mutagenesis genetic diversity S. cerevisiae through different

Language: Английский

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